Literature DB >> 35675815

A conceptual framework for understanding phase separation and addressing open questions and challenges.

Tanja Mittag1, Rohit V Pappu2.   

Abstract

Macromolecular phase separation is being recognized for its potential importance and relevance as a driver of spatial organization within cells. Here, we describe a framework based on synergies between networking (percolation or gelation) and density (phase separation) transitions. Accordingly, the phase transitions in question are referred to as phase separation coupled to percolation (PSCP). The condensates that result from PSCP are viscoelastic network fluids. Such systems have sequence-, composition-, and topology-specific internal network structures that give rise to time-dependent interplays between viscous and elastic properties. Unlike pure phase separation, the process of PSCP gives rise to sequence-, chemistry-, and structure-specific distributions of clusters that can form at concentrations that lie well below the threshold concentration for phase separation. PSCP, influenced by specific versus solubility-determining interactions, also provides a bridge between different observations and helps answer questions and address challenges that have arisen regarding the role of macromolecular phase separation in biology.
Copyright © 2022 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  associative polymers; biomolecular condensate; biophysics; cell biology; cluster; membraneless organelle; network fluid; percolation; phase separation; saturation concentration; viscoelasticity

Year:  2022        PMID: 35675815      PMCID: PMC9233049          DOI: 10.1016/j.molcel.2022.05.018

Source DB:  PubMed          Journal:  Mol Cell        ISSN: 1097-2765            Impact factor:   19.328


  117 in total

1.  A human interactome in three quantitative dimensions organized by stoichiometries and abundances.

Authors:  Marco Y Hein; Nina C Hubner; Ina Poser; Jürgen Cox; Nagarjuna Nagaraj; Yusuke Toyoda; Igor A Gak; Ina Weisswange; Jörg Mansfeld; Frank Buchholz; Anthony A Hyman; Matthias Mann
Journal:  Cell       Date:  2015-10-22       Impact factor: 41.582

2.  Phase-separation mechanism for C-terminal hyperphosphorylation of RNA polymerase II.

Authors:  Huasong Lu; Dan Yu; Anders S Hansen; Sourav Ganguly; Rongdiao Liu; Alec Heckert; Xavier Darzacq; Qiang Zhou
Journal:  Nature       Date:  2018-05-30       Impact factor: 49.962

3.  Composition-dependent thermodynamics of intracellular phase separation.

Authors:  Joshua A Riback; Lian Zhu; Mylene C Ferrolino; Michele Tolbert; Diana M Mitrea; David W Sanders; Ming-Tzo Wei; Richard W Kriwacki; Clifford P Brangwynne
Journal:  Nature       Date:  2020-05-06       Impact factor: 49.962

4.  Release of linker histone from the nucleosome driven by polyelectrolyte competition with a disordered protein.

Authors:  Pétur O Heidarsson; Davide Mercadante; Andrea Sottini; Daniel Nettels; Madeleine B Borgia; Alessandro Borgia; Sinan Kilic; Beat Fierz; Robert B Best; Benjamin Schuler
Journal:  Nat Chem       Date:  2022-01-06       Impact factor: 24.274

5.  Phase transitions in the assembly of multivalent signalling proteins.

Authors:  Pilong Li; Sudeep Banjade; Hui-Chun Cheng; Soyeon Kim; Baoyu Chen; Liang Guo; Marc Llaguno; Javoris V Hollingsworth; David S King; Salman F Banani; Paul S Russo; Qiu-Xing Jiang; B Tracy Nixon; Michael K Rosen
Journal:  Nature       Date:  2012-03-07       Impact factor: 49.962

6.  Phase transition of a disordered nuage protein generates environmentally responsive membraneless organelles.

Authors:  Timothy J Nott; Evangelia Petsalaki; Patrick Farber; Dylan Jervis; Eden Fussner; Anne Plochowietz; Timothy D Craggs; David P Bazett-Jones; Tony Pawson; Julie D Forman-Kay; Andrew J Baldwin
Journal:  Mol Cell       Date:  2015-03-05       Impact factor: 17.970

7.  Pol II phosphorylation regulates a switch between transcriptional and splicing condensates.

Authors:  Yang Eric Guo; John C Manteiga; Jonathan E Henninger; Benjamin R Sabari; Alessandra Dall'Agnese; Nancy M Hannett; Jan-Hendrik Spille; Lena K Afeyan; Alicia V Zamudio; Krishna Shrinivas; Brian J Abraham; Ann Boija; Tim-Michael Decker; Jenna K Rimel; Charli B Fant; Tong Ihn Lee; Ibrahim I Cisse; Phillip A Sharp; Dylan J Taatjes; Richard A Young
Journal:  Nature       Date:  2019-08-07       Impact factor: 49.962

8.  Sequence-encoded and composition-dependent protein-RNA interactions control multiphasic condensate morphologies.

Authors:  Muralikrishna Raju; Ibraheem Alshareedah; Taranpreet Kaur; Richoo B Davis; Davit A Potoyan; Priya R Banerjee
Journal:  Nat Commun       Date:  2021-02-08       Impact factor: 14.919

9.  Ligand effects on phase separation of multivalent macromolecules.

Authors:  Kiersten M Ruff; Furqan Dar; Rohit V Pappu
Journal:  Proc Natl Acad Sci U S A       Date:  2021-03-09       Impact factor: 11.205

10.  Deciphering how naturally occurring sequence features impact the phase behaviours of disordered prion-like domains.

Authors:  Anne Bremer; Mina Farag; Wade M Borcherds; Ivan Peran; Erik W Martin; Rohit V Pappu; Tanja Mittag
Journal:  Nat Chem       Date:  2021-12-20       Impact factor: 24.274

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  6 in total

Review 1.  Organization, dynamics and mechanoregulation of integrin-mediated cell-ECM adhesions.

Authors:  Pakorn Kanchanawong; David A Calderwood
Journal:  Nat Rev Mol Cell Biol       Date:  2022-09-27       Impact factor: 113.915

2.  An Interpretable Machine-Learning Algorithm to Predict Disordered Protein Phase Separation Based on Biophysical Interactions.

Authors:  Hao Cai; Robert M Vernon; Julie D Forman-Kay
Journal:  Biomolecules       Date:  2022-08-17

Review 3.  Micellization: A new principle in the formation of biomolecular condensates.

Authors:  Tomohiro Yamazaki; Tetsuya Yamamoto; Tetsuro Hirose
Journal:  Front Mol Biosci       Date:  2022-08-29

4.  Double-stranded RNA drives SARS-CoV-2 nucleocapsid protein to undergo phase separation at specific temperatures.

Authors:  Christine A Roden; Yifan Dai; Catherine A Giannetti; Ian Seim; Myungwoon Lee; Rachel Sealfon; Grace A McLaughlin; Mark A Boerneke; Christiane Iserman; Samuel A Wey; Joanne L Ekena; Olga G Troyanskaya; Kevin M Weeks; Lingchong You; Ashutosh Chilkoti; Amy S Gladfelter
Journal:  Nucleic Acids Res       Date:  2022-08-12       Impact factor: 19.160

5.  Coevolution of the Ess1-CTD axis in polar fungi suggests a role for phase separation in cold tolerance.

Authors:  Ryan J Palumbo; Nathan McKean; Erinn Leatherman; Kevin E W Namitz; Laurie Connell; Aaron Wolfe; Kelsey Moody; Cene Gostinčar; Nina Gunde-Cimerman; Alaji Bah; Steven D Hanes
Journal:  Sci Adv       Date:  2022-09-07       Impact factor: 14.957

Review 6.  Aging RNA granule dynamics in neurodegeneration.

Authors:  Kevin Rhine; Norah Al-Azzam; Tao Yu; Gene W Yeo
Journal:  Front Mol Biosci       Date:  2022-09-16
  6 in total

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